@article {Radice2016,
	title = {{Vertical water mass structure in the North Atlantic influences the bathymetric distribution of species in the deep-sea coral genus Paramuricea}},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	volume = {116},
	year = {2016},
	pages = {253{\textendash}263},
	abstract = {Deep-sea corals are the structural foundation of their ecosystems along continental margins worldwide, yet the factors driving their broad distribution are poorly understood. Environmental factors, especially depth-related variables including water mass properties, are thought to considerably affect the realized distribution of deep-sea corals. These factors are governed by local and regional oceanographic conditions that directly influence the dispersal of larvae, and therefore affect the ultimate distribution of adult corals. We used molecular barcoding of mitochondrial and nuclear sequences to identify species of octocorals in the genus Paramuricea collected from the Labrador Sea to the Grand Banks of Newfoundland, Canada at depths of 150{\textendash}1500 m. The results of this study revealed overlapping bathymetric distributions of the Paramuricea species present off the eastern Canadian coast, including the presence of a few cryptic species previously designated as Paramuricea placomus. The distribution of Paramuricea species in the western North Atlantic differs from the Gulf of Mexico, where five Paramuricea species exhibit strong segregation by depth. The different patterns of Paramuricea species in these contrasting biogeographic regions provide insight into how water mass structure may shape species distribution. Investigating Paramuricea prevalence and distribution in conjunction with oceanographic conditions can help demonstrate the factors that generate and maintain deep-sea biodiversity.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1016/j.dsr.2016.08.014},
	author = {Radice, V Z and Quattrini, A M and Wareham, V E and Edinger, E N and Cordes, E E}
}
@article {Quattrini2015,
	title = {{Testing the depth-differentiation hypothesis in a deepwater octocoral}},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {282},
	number = {1807},
	year = {2015},
	pages = {20150008},
	abstract = {The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200-1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species commonly occurs throughout the northern Gulf of Mexico at depths ranging from 400 to 900 m. We found significant genetic differentiation (FST = 0.042) across seven sites spanning 400 km of distance and 400 m of depth. A pattern of isolation by depth emerged, but geographical distance between sites may further limit gene flow. Water mass boundaries may serve to isolate populations across depth; however, adaptive divergence with depth is also a possible scenario. Microsatellite markers also revealed significant genetic differentiation (FST = 0.434) between C. delta and a closely related species, Callogorgia americana, demonstrating the utility of microsatellites in species delimitation of octocorals. Results provided support for the depth-differentiation hypothesis, strengthening the notion that factors covarying with depth serve as isolation mechanisms in deep-sea populations.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1098/rspb.2015.0008},
	author = {Quattrini, A M and Baums, I B and Shank, T M and Morrison, C and Cordes, E E}
}
@article {Doughty2014,
	title = {{Insights into the population dynamics of the deep-sea coral genus Paramuricea in the Gulf of Mexico}},
	journal = {Biology and Geology of Deep-Sea Coral Ecosystems: Proceedings of the Fifth International Symposium on Deep Sea Corals},
	volume = {99},
	year = {2014},
	pages = {71{\textendash}82},
	abstract = {Species in the genus Paramuricea are among the most common corals in deep waters ({\textgreater}200~m) of the Gulf of Mexico. Paramuricea spp. increase habitat heterogeneity and provide substrate for numerous faunal associates, including ophiuroids that occur on the majority of coral colonies. In light of the Deepwater Horizon oil spill in the Gulf of Mexico, it has become apparent that there is a critical need for data on population dynamics within this genus. To date, at least one species of Paramuricea (P. biscaya) is known to be negatively impacted by the spill. Using remotely operated vehicles from 2009 to 2011, we documented the density and size frequency distributions of Paramuricea across 21 sites at depths of 250{\textendash}2500~m. Molecular barcoding (mtCOI+igr+MutS) was used to delineate species boundaries among the specimens collected. Results suggested that seven haplotypes are present in the Gulf, and appear to be partially segregated by depth [(type H: was used to delineate species boundaries among the specimens collected. Results suggested that seven haplotypes are present in the Gulf, and appear to be partially segregated by depth [(type H: Paramuricea spp. determined by ROV surveys were mapped onto high-resolution bathymetric data, which confirmed the corals{\textquoteright} preference for topographic highs composed of hard substrata. At any one site, densities ranged from 0.043{\textpm}0.01 (VK906, 380~m) to 1.18{\textpm}0.81~colonies/m2 (GC852, 1410~m). Mortality and recruitment rates were estimated from size-frequency data combined with estimated growth rates. Mortality rate decreased with size, from approximately 20{\%} and 70{\%} in new recruits of Paramuricea B3 and P. biscaya respectively, to less than 10{\%} in colonies over 40~cm in both species. Recruitment rates were estimated from less than one to over 30 individuals per year per site, but patterns in size-frequency histograms suggest that this process is highly variable at the different sites and at different times. These data illustrate that populations of the slow-growing Paramuricea species are sparsely distributed and exhibit low recruitment rates, making them highly susceptible to anthropogenic threats.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2013.05.023},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064513002142},
	author = {Doughty, C L and Quattrini, A M and Cordes, E E}
}
@article {Quattrini2014,
	title = {{A phylogenetic approach to octocoral community structure in the deep Gulf of Mexico}},
	journal = {Biology and Geology of Deep-Sea Coral Ecosystems: Proceedings of the Fifth International Symposium on Deep Sea Corals},
	volume = {99},
	year = {2014},
	pages = {92{\textendash}102},
	abstract = {{Deep-sea communities are becoming increasingly vulnerable to anthropogenic disturbances, as fishing, hydrocarbon exploration and extraction, and mining activities extend into deeper water. Negative impacts from such activities were recently documented in the Gulf of Mexico (GoM), where the Deepwater Horizon oil spill caused substantial damage to a deep-water octocoral community. Although a faunal checklist and numerous museum records are currently available for the entire GoM, local-scale diversity and assemblage structure of octocoral communities remains unknown, particularly in deep water. On a series of recent cruises (2008{\textendash}2011) using remotely operated vehicles, 435 octocorals were collected from 33 deep-water sites (250{\textendash}2500~m) in the northern GoM. To elucidate species boundaries, the extended mitochondrial barcode (COI+igr1+msh) was successfully amplified and sequenced for 422 of these specimens, yielding a total of 64 haplotypes representing at least 52 species. Further, at least 29{\%} of the species collected were either previously not known to occur in the GoM (12 species) or represent new species (at least three species). Overall, species richness at each site was fairly low (1{\textendash}12 spp.). The greatest species richness occurred at the shallowest () was successfully amplified and sequenced for 422 of these specimens, yielding a total of 64 haplotypes representing at least 52 species. Further, at least 29{\%} of the species collected were either previously not known to occur in the GoM (12 species) or represent new species (at least three species). Overall, species richness at each site was fairly low (1{\textendash}12 spp.). The greatest species richness occurred at the shallowest (n=8 spp.) and the deepest (2100{\textendash}2500~m: DC673},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2013.05.027},
	url = {http://www.sciencedirect.com/science/article/pii/S096706451300218X},
	author = {Quattrini, A M and Etnoyer, P J and Doughty, C and English, Lisa and Falco, R and Remon, N and Rittinghouse, M and Cordes, E E}
}
@article {Feng2013,
	title = {{A comparative study of authigenic carbonates from mussel and tubeworm environments: Implications for discriminating the effects of tubeworms}},
	journal = {Deep-Sea Research. Part I: Oceanographic Research Papers},
	volume = {75},
	year = {2013},
	pages = {110{\textendash}118},
	abstract = {The Gulf of Mexico hydrocarbon seeps are often populated by dense mussel beds and tubeworm aggregations, as well as exposed authigenic carbonate outcrops. Previous studies suggest the activity of mussels and tubeworms could influence the sediment geochemistry of their habitats, resulting in variations in the stable carbon isotopes of the associated carbonates. However, this conclusion was based on the analyses of samples from a single site. To better understand whether there are consistent differences in the geochemical environments of mussels and tubeworms, mineralogical and stable isotopic compositions of authigenic carbonates from mussel and tubeworm environments from four seep sites were analyzed. The studied sites span a depth range of 1200~m to 2800~m on the northern Gulf of Mexico continental slope. We found that carbonate samples from tubeworm environments were more prone to contain aragonite whereas carbonates from mussel environments were more likely to have calcite. This finding supports the hypothesis that vestimentiferans release sulfate across their roots into the pore waters of the surrounding sediments, a process that could generate a locally sulfate-enriched environment that favors the precipitation of aragonite instead of calcite. Moreover, the $δ$13C values of tubeworm carbonates are generally lighter than that of mussel carbonates from the same site, which is consistent with the fact that tubeworms are fueling extra subsurface methane oxidation through the release of sulfate into the sediment. Such a process, consequently, enriches the subsurface dissolved inorganic carbon pool with light carbon derived from the seeping hydrocarbons. Taken together, our data suggest that tubeworms could produce a carbon isotope shift that is sufficient to influence the sediment geochemistry of their immediate area, and that this impact is reflected in the associated authigenic carbonates.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0637},
	doi = {10.1016/j.dsr.2013.02.002},
	url = {http://www.sciencedirect.com/science/article/pii/S0967063713000435},
	author = {Feng, D and Cordes, E E and Roberts, H H and Fisher, C R}
}
@article {White2012,
	title = {{Impact of the Deepwater Horizon oil spill on a deep-water coral community in the Gulf of Mexico}},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	number = {50},
	year = {2012},
	month = {dec},
	pages = {20303{\textendash}20308},
	abstract = {To assess the potential impact of the Deepwater Horizon oil spill on offshore ecosystems, 11 sites hosting deep-water coral communities were examined 3 to 4 mo after the well was capped. Healthy coral communities were observed at all sites {\textgreater}20 km from the Macondo well, including seven sites previously visited in September 2009, where the corals and communities appeared unchanged. However, at one site 11 km southwest of the Macondo well, coral colonies presented widespread signs of stress, including varying degrees of tissue loss, sclerite enlargement, excess mucous production, bleached commensal ophiuroids, and covering by brown flocculent material (floc). On the basis of these criteria the level of impact to individual colonies was ranked from 0 (least impact) to 4 (greatest impact). Of the 43 corals imaged at that site, 46{\%} exhibited evidence of impact on more than half of the colony, whereas nearly a quarter of all of the corals showed impact to {\textgreater}90{\%} of the colony. Additionally, 53{\%} of these corals{\textquoteright} ophiuroid associates displayed abnormal color and/or attachment posture. Analysis of hopanoid petroleum biomarkers isolated from the floc provides strong evidence that this material contained oil from the Macondo well. The presence of recently damaged and deceased corals beneath the path of a previously documented plume emanating from the Macondo well provides compelling evidence that the oil impacted deep-water ecosystems. Our findings underscore the unprecedented nature of the spill in terms of its magnitude, release at depth, and impact to deep-water ecosystems.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0027-8424},
	doi = {10.1073/pnas.1118029109},
	author = {White, H K and Hsing, P-Y and Cho, W and Shank, T M and Cordes, E E and Quattrini, A M and Nelson, R K and Camilli, R and Demopoulos, A W J and German, C R and Brooks, J M and Roberts, H H and Shedd, W and Reddy, C M and Fisher, C R}
}
@article {Lessard-Pilon2010,
	title = {{Community composition and temporal change at deep Gulf of Mexico cold seeps}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {57},
	number = {21-23},
	year = {2010},
	pages = {1891{\textendash}1903},
	abstract = {Specialized cold-seep communities have been known to exist in the Gulf of Mexico (GOM) since the mid-1980s, but only recently has extensive research been carried out on sites at depths {\textgreater}1000 m. This study uses a combination of imagery and analyses within a Geographic Information Systems (GIS) framework to examine the composition of mussel and tubeworm communities at depths between 2200 and 2800 m in the Gulf of Mexico, spatial relations among the fauna, and changes in these communities over time. Photomosaics at three discrete seep communities were obtained in 2006 and a video mosaic of another community was obtained in 1992. Each of these communities was re-imaged in 2007. In addition, quantitative physical collections were made within two of the photomosaic sites and used to confirm the identification of megafauna, quantify the occurrence of smaller and cryptic macrofauna, and allow first-order calculations of biomass within the sites. Substrate type had a significant effect on community composition. Significant associations were identified between live mussels with anemones, shrimp, and sea cucumbers, and between tubeworm aggregations and Munidopsis sp. crabs and encrusting fauna, indicating differences in the composition of megafauna associated with adjacent mussel and tubeworm aggregations. Little change was seen in the total area colonized by foundation fauna (tubeworms and mussels) between years at any site. However, significant changes occurred in the positions of mussels, even over periods of a single year, at all sites, and evidence for the establishment of new tubeworm aggregations between 1992 and 2007 was noted at one site. These photomosaics provide data suggesting that environmental conditions can change over small spatial and temporal scales and mussels move in response to these changes. The successional trends are examined and compared to the patterns that have been documented in shallow ({\textless}1000-m depth) Gulf of Mexico seep communities.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2010.05.012},
	url = {http://dx.doi.org/10.1016/j.dsr2.2010.05.012},
	author = {Lessard-Pilon, S and Porter, M D and Cordes, E E and MacDonald, I R and Fisher, C R}
}
@article {Levin2010,
	title = {{Diversity of bathyal macrofauna on the northeastern Pacific margin: the influence of methane seeps and oxygen minimum zones}},
	journal = {Marine Ecology},
	volume = {31},
	number = {1},
	year = {2010},
	pages = {94{\textendash}110},
	publisher = {Blackwell Publishing Ltd},
	abstract = {The upper continental slope in the northeastern Pacific Ocean is intercepted by a deep oxygen minimum zone (OMZ; 650{\textendash}1100 m) and punctuated by conduits of methane seepage. We examined the effects of these two dominant sources of heterogeneity on the density, composition and diversity of heterotrophic macrofauna off Hydrate Ridge, Oregon (OR; 800 m water depth), where the seeps co-occur within an OMZ, and off the Eel River, Northern California (CA; 500 m), where seeps are overlain by better oxygenated waters. We hypothesized that seeps (containing clam beds and microbial mats) should contribute a suite of distinct species to the regional margin species pool but that OMZ-associated hypoxia would dampen seep-related heterogeneity. Macrofaunal densities were highest (23,000{\textendash}33,510 ind{\textperiodcentered}m-2) in the CA seep sediments and in the OR near-seep samples, intermediate in the OR seep, CA near seep and CA and OR 500-m margin sediments (10,054{\textendash}19,777 ind{\textperiodcentered}m-2), and lowest in the CA and OR OMZ habitats at 800 m (4269{\textendash}7847 ind{\textperiodcentered}m-2). Annelids constituted over 50{\%} of the taxa in all but the CA clam bed and OR microbial mat sediments, where mollusks were abundant. Approximately 50{\%} of seep species appeared to be habitat endemic; species present in microbial mats largely formed a subset of those present in the clam beds. Dorvilleid and ampharetid polychaetes were dominant in the seep sediments; non-seep margin sediments at 500 and 800 m were populated heavily by branchiate polychaetes including cossurids and paraonids. Alpha diversity (Es[20] calculated per core) was lowest and rank 1 dominance was highest in the CA and OR microbial mat habitats. Pooled analyses of Es[100] revealed highest species richness in the CA clam bed and near-seep habitats (30.3 and 29.6, respectively), and lowest species richness in the OR microbial mat and near-seep habitats (16.5 and 17.9, respectively). Non-seep sediments (500 and 800 m) off both CA and OR were more homogeneous (55{\textendash}57{\%} within-habitat similarity) than clam bed and microbial mat sediments (only 32{\textendash}37{\%} within-habitat similarity). CA sediment macrofauna generally exhibit higher alpha diversity, and as habitats are combined, a higher rate of increase in the slope of the species accumulation curves than do OR margin macrofauna. Methane seeps in the NE Pacific introduce significant heterogeneity that increases margin biodiversity at multiple spatial scales. However, our hypothesis that the OMZ would lessen the seep contributions to diversity was not supported. The better oxygenated CA seeps at 500 m shared more of the background margin fauna (at 500 m) than did the OR seeps at 800 m (with OMZ fauna at 800 m). Geographical differences in the fluxes of methane-rich fluids and the increased reliance on chemosynthetic food sources with increased depth could explain these results.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1439-0485},
	doi = {10.1111/j.1439-0485.2009.00335.x},
	url = {http://dx.doi.org/10.1111/j.1439-0485.2009.00335.x},
	author = {Levin, L A and Mendoza, G F and Gonzalez, J P and Thurber, A R and Cordes, E E}
}
@article {Bright2010,
	title = {{Epizooic metazoan meiobenthos associated with tubeworm and mussel aggregations from cold seeps of the northern Gulf of Mexico}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {57},
	number = {21-23},
	year = {2010},
	pages = {1982{\textendash}1989},
	abstract = {The abundance and higher taxonomic composition of epizooic metazoan meiobenthic communities associated with mussel and tubeworm aggregations of hydrocarbon seeps at Green Canyon, Atwater Valley, and Alaminos Canyon in depths between 1400 and 2800 m were studied and compared to the infaunal community of non-seep sediments nearby. Epizooic meiofaunal abundances of associated meiobenthos living in tubeworm bushes and mussel beds at seeps were extremely low (usually {\textless}100 ind. 10 cm-2), similar to epizooic meiofauna at deep-sea hydrothermal vents, and the communities were composed primarily of nematodes, copepods, ostracods, and halacarids. In contrast, epizooic meiobenthic abundance is lower than previous studies have reported for infauna from seep sediments. Interestingly, non-seep sediments contained higher abundances and higher taxonomic diversity than epizooic seep communities, although in situ primary production is restricted to seeps.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2010.05.003},
	url = {http://dx.doi.org/10.1016/j.dsr2.2010.05.003},
	author = {Bright, M and Plum, C and Riavitz, L A and Arbizu, P M and Cordes, E E and Gollner, S}
}
@article {Cordes2010,
	title = {{Influence of foundation species, depth, and location on diversity and community composition at Gulf of Mexico lower-slope cold seeps}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {57},
	number = {21-23},
	year = {2010},
	pages = {1870{\textendash}1881},
	abstract = {Efforts to understand and preserve the seep communities of the deep Gulf of Mexico (GOM) begin with a comprehensive survey of the biodiversity of these communities. Previous studies have provided a conceptual model of the physiology, population, and community ecology of upper continental slope seeps. However, seeps at water depths below 1000 m in the Gulf of Mexico remain relatively unknown. In this study, data from 47 samples of tubeworm- and mussel-associated communities at depths of 1005{\textendash}2750 m are examined. Other than tubeworms and mussels, 66 taxa of macro- and megafauna were collected, 43 of which appear to be restricted to water depths of over 1000 m, and 39 that have not been reported previously from the Gulf of Mexico. Diversity in mussel beds was highest at mid-slope depths, but tubeworm-associated communities did not show clear bathymetric trends in diversity. Diversity was higher in tubeworm aggregations at the alpha level (per sample), but higher in mussel beds at the beta level (species turnover among collections). Although both community types were often numerically dominated by the endemic shrimp Alvinocaris muricola, broad differences in the communities hosted by tubeworm aggregations and mussel beds were apparent. The most important factors explaining community similarity within community type were the depth, relative abundance of different mussel species in a bed, and the average size of tubeworms in an aggregation. The high proportion of deep-seep species that were found for the first time in the Gulf of Mexico emphasizes the importance of conservation efforts for these patchy communities.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2010.05.010},
	url = {http://dx.doi.org/10.1016/j.dsr2.2010.05.010},
	author = {Cordes, E E and Becker, E L and Hourdez, S and Fisher, C R}
}
@article {Becker2009,
	title = {{Importance of seep primary production to Lophelia pertusa and associated fauna in the Gulf of Mexico}},
	journal = {Deep-Sea Research. Part I: Oceanographic Research Papers},
	volume = {56},
	number = {5},
	year = {2009},
	pages = {786{\textendash}800},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0637},
	doi = {10.1016/j.dsr.2008.12.006},
	url = {http://dx.doi.org/10.1016/j.dsr.2008.12.006},
	author = {Becker, E L and Cordes, E E and Macko, S A and Fisher, C R}
}
